Abstract Development of cartilage, bones, muscles, tendons and ligaments must be highly coordinated, with tissue type differentiation and morphogenesis occuring in a concerted way that allows the resulting tissues to function together. The axial musculoskeleton (vertebral column and ribs) develops from the somites, in which all musculoskeletal tissue types are specified and develop coordinately. However, the morphology of somite derivatives varies with position along the body axis. This variation is controlled by Hox proteins, conserved transcription factors that pattern the body axis of most animal embryos. In vertebrates, Hox proteins both confer anterior-posterior identity on nascent segments and play direct roles in tissue morphogenesis later in development. However, we still know relatively little about their mechanisms of action, including the cell and tissue types in which they act, the cellular behaviors they regulate, and ultimately their transcriptional targets. Hoxa5 non-redundantly patterns musculoskeletal elements at the cervical-thoracic transition. In order to understand how it acts, we used genetic lineage labeling to fate map the descendants of Hoxa5 expressing cells. We found that Hoxa5 descendants contribute to a restricted number tissue types, such as cartilage and perichondrium, but only contribute rarely to tendon and never to muscle. This restriction of Hoxa5 descendant fate may reflect an important aspect of its function. Here, we propose to investigate the mechanism through which Hoxa5 patterns the cervical-thoracic transition musculoskeleton of mice, using a combination of genetic lineage labeling, conditional and loss-of-function analysis, and high throughput sequencing. Our specific aims are designed to: (1) Identify the tissue specificity of Hoxa5 action in patterning the axial skeleton (2) Identify genes and gene networks regulated cell-autonomously by Hoxa5 and (3) Identify direct transcriptional targets of Hoxa5 in the somites. Successful completion of this project will shed light on the mechanisms through which axial patterning is regulated by Hox genes, and can also be applied to a general understanding the mechanisms of Hoxa5 in other tissue types and cancers. More generally, the work is relevant to human health through its application to understanding musculoskeletal tissue patterning and differentiation during normal development and disease. Finally, this work will be conducted with undergraduates at Barnard College, a liberal arts college for women. It will be performed by research students in the PI?s lab, and will be introduced into a newly developed, full year laboratory course at Barnard. Course-based research has been shown to increase participation of students, including those from underrepresented groups, in STEM and to increase the pursuit of postgraduate STEM training. This course will engage undergraduates in substantive original research while providing them with training in current molecular genetics approaches.